Whatever is the overpowered godship of the release, provided it is not too annoying to pilot. In old releases before 0.7, it was Hyperion or Medusa. During 0.7, it was Onslaught. During 0.8, it was either Astral or Paragon. During early 0.9, it was Harbinger (when it could use medium Reapers). During 0.95, it was Doom (when it had long-range mines with Systems Expertise). Today, it is Ziggurat. Honorable mention to Afflictor chains, though it is annoying to pilot at times because mistakes are unforgiving (and enemy phase frigates that stall and drain PPT are annoying to fight with a phase frigate.)
Ziggurat with Omega weapons is about as overpowered as 0.7 era Onslaught, although 0.7 Onslaught had the benefit of stronger skills and much less cowardly enemy AI that did not hesitate drifting into Onslaught's superior shot range instead of waiting until mutual CR timeout.
Aside from that, I prefer bigger ships with lots of guns because many other shoot-'em-up games (arcade games, Star Control, Transcendence) put the player in a fighter craft or mech (or equivalent) with a single (or dual) forward-facing (or occasionally spread) gun, while enemies are either other fighter craft or big battleship boss.
About phase ships. I prefer pre-0.72 original style phase cloak with no cooldown. That style works great for brawling phase ships. Ziggurat works similar to that style, it is the only phase ship that can truly brawl. Other phase ships with normal phase cloaks are suited only for assassination, but since the speed loss of 0.95.1, only frigates are fast enough for the job. AI cannot pilot Harbinger effectively (because it always tries its assassination path, but it is too slow to pull it off). Now, Doom needs lots of skills (especially elite Field Mod. and Systems Exp.) to match its pre-nerf power and mine things from long enough range.